A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
This report has been generated by the bigbio/quantms analysis pipeline. For information about how to interpret these results, please see the documentation.
Report
generated on 2025-04-23, 10:48 UTC
based on data in:
/home/runner/work/pmultiqc/pmultiqc/data
pmultiqc
pmultiqc is a MultiQC module to show the pipeline performance of mass spectrometry based quantification pipelines such as nf-core/quantms, MaxQuant.URL: https://github.com/bigbio/pmultiqc
Experimental Design
This table shows the design of the experiment. I.e., which files and channels correspond to which sample/condition/fraction.
You can see details about it in https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/classOpenMS_1_1ExperimentalDesign.html
| Sample Name | MSstats Condition: SP | MSstats Condition: CT | MSstats Condition: QY | MSstats Condition: CV | MSstats BioReplicate | Fraction Group | Fraction | Label |
|---|---|---|---|---|---|---|---|---|
| 1 | Saccharomyces cerevisiae | Mixture | 10% | in-house | 1 | |||
| 1 | 1 | 1 | ||||||
| 1 | 2 | 1 | ||||||
| 1 | 3 | 1 | ||||||
| 1 | 4 | 1 | ||||||
| 1 | 5 | 1 | ||||||
| 1 | 6 | 1 | ||||||
| 1 | 7 | 1 | ||||||
| 1 | 8 | 1 | ||||||
| 1 | 9 | 1 | ||||||
| 1 | 10 | 1 | ||||||
| 1 | 11 | 1 | ||||||
| 2 | Saccharomyces cerevisiae | Mixture | 10% | in-house | 2 | |||
| 1 | 1 | 2 | ||||||
| 1 | 2 | 2 | ||||||
| 1 | 3 | 2 | ||||||
| 1 | 4 | 2 | ||||||
| 1 | 5 | 2 | ||||||
| 1 | 6 | 2 | ||||||
| 1 | 7 | 2 | ||||||
| 1 | 8 | 2 | ||||||
| 1 | 9 | 2 | ||||||
| 1 | 10 | 2 | ||||||
| 1 | 11 | 2 | ||||||
| 3 | Saccharomyces cerevisiae | Mixture | 10% | in-house | 3 | |||
| 1 | 1 | 3 | ||||||
| 1 | 2 | 3 | ||||||
| 1 | 3 | 3 | ||||||
| 1 | 4 | 3 | ||||||
| 1 | 5 | 3 | ||||||
| 1 | 6 | 3 | ||||||
| 1 | 7 | 3 | ||||||
| 1 | 8 | 3 | ||||||
| 1 | 9 | 3 | ||||||
| 1 | 10 | 3 | ||||||
| 1 | 11 | 3 | ||||||
| 4 | Saccharomyces cerevisiae | Mixture | 5% | in-house | 4 | |||
| 1 | 1 | 4 | ||||||
| 1 | 2 | 4 | ||||||
| 1 | 3 | 4 | ||||||
| 1 | 4 | 4 | ||||||
| 1 | 5 | 4 | ||||||
| 1 | 6 | 4 | ||||||
| 1 | 7 | 4 | ||||||
| 1 | 8 | 4 | ||||||
| 1 | 9 | 4 | ||||||
| 1 | 10 | 4 | ||||||
| 1 | 11 | 4 | ||||||
| 5 | Saccharomyces cerevisiae | Mixture | 5% | in-house | 5 | |||
| 1 | 1 | 5 | ||||||
| 1 | 2 | 5 | ||||||
| 1 | 3 | 5 | ||||||
| 1 | 4 | 5 | ||||||
| 1 | 5 | 5 | ||||||
| 1 | 6 | 5 | ||||||
| 1 | 7 | 5 | ||||||
| 1 | 8 | 5 | ||||||
| 1 | 9 | 5 | ||||||
| 1 | 10 | 5 | ||||||
| 1 | 11 | 5 | ||||||
| 6 | Saccharomyces cerevisiae | Mixture | 5% | in-house | 6 | |||
| 1 | 1 | 6 | ||||||
| 1 | 2 | 6 | ||||||
| 1 | 3 | 6 | ||||||
| 1 | 4 | 6 | ||||||
| 1 | 5 | 6 | ||||||
| 1 | 6 | 6 | ||||||
| 1 | 7 | 6 | ||||||
| 1 | 8 | 6 | ||||||
| 1 | 9 | 6 | ||||||
| 1 | 10 | 6 | ||||||
| 1 | 11 | 6 | ||||||
| 7 | Saccharomyces cerevisiae | Mixture | 5% | in-house | 7 | |||
| 1 | 1 | 7 | ||||||
| 1 | 2 | 7 | ||||||
| 1 | 3 | 7 | ||||||
| 1 | 4 | 7 | ||||||
| 1 | 5 | 7 | ||||||
| 1 | 6 | 7 | ||||||
| 1 | 7 | 7 | ||||||
| 1 | 8 | 7 | ||||||
| 1 | 9 | 7 | ||||||
| 1 | 10 | 7 | ||||||
| 1 | 11 | 7 | ||||||
| 8 | Saccharomyces cerevisiae | Mixture | 3.3% | in-house | 8 | |||
| 1 | 1 | 8 | ||||||
| 1 | 2 | 8 | ||||||
| 1 | 3 | 8 | ||||||
| 1 | 4 | 8 | ||||||
| 1 | 5 | 8 | ||||||
| 1 | 6 | 8 | ||||||
| 1 | 7 | 8 | ||||||
| 1 | 8 | 8 | ||||||
| 1 | 9 | 8 | ||||||
| 1 | 10 | 8 | ||||||
| 1 | 11 | 8 | ||||||
| 9 | Saccharomyces cerevisiae | Mixture | 3.3% | in-house | 9 | |||
| 1 | 1 | 9 | ||||||
| 1 | 2 | 9 | ||||||
| 1 | 3 | 9 | ||||||
| 1 | 4 | 9 | ||||||
| 1 | 5 | 9 | ||||||
| 1 | 6 | 9 | ||||||
| 1 | 7 | 9 | ||||||
| 1 | 8 | 9 | ||||||
| 1 | 9 | 9 | ||||||
| 1 | 10 | 9 | ||||||
| 1 | 11 | 9 | ||||||
| 10 | Saccharomyces cerevisiae | Mixture | 3.3% | in-house | 10 | |||
| 1 | 1 | 10 | ||||||
| 1 | 2 | 10 | ||||||
| 1 | 3 | 10 | ||||||
| 1 | 4 | 10 | ||||||
| 1 | 5 | 10 | ||||||
| 1 | 6 | 10 | ||||||
| 1 | 7 | 10 | ||||||
| 1 | 8 | 10 | ||||||
| 1 | 9 | 10 | ||||||
| 1 | 10 | 10 | ||||||
| 1 | 11 | 10 | ||||||
| 11 | Saccharomyces cerevisiae | Mixture | 3.3% | in-house | 11 | |||
| 1 | 1 | 11 | ||||||
| 1 | 2 | 11 | ||||||
| 1 | 3 | 11 | ||||||
| 1 | 4 | 11 | ||||||
| 1 | 5 | 11 | ||||||
| 1 | 6 | 11 | ||||||
| 1 | 7 | 11 | ||||||
| 1 | 8 | 11 | ||||||
| 1 | 9 | 11 | ||||||
| 1 | 10 | 11 | ||||||
| 1 | 11 | 11 |
MS1 Information
MS1 quality control information extracted from the spectrum files
This plot displays Total Ion Chromatograms (TICs) derived from MS1 scans across all analyzed samples. The x-axis represents retention time, and the y-axis shows the total ion intensity at each time point. Each colored trace corresponds to a different sample. The TIC provides a global view of the ion signal throughout the LC-MS/MS run, reflecting when compounds elute from the chromatography column. Key aspects to assess include:
- Overall intensity pattern: A consistent baseline and similar peak profiles across samples indicate good reproducibility.
- Major peak alignment: Prominent peaks appearing at similar retention times suggest stable chromatographic performance.
- Signal-to-noise ratio: High peaks relative to baseline noise reflect better sensitivity.
- Chromatographic resolution: Sharp, well-separated peaks indicate effective separation.
- Signal drift: A gradual decline in signal intensity across the run may point to source contamination or chromatography issues.
Deviations such as shifted retention times, missing peaks, or inconsistent intensities may signal problems in sample preparation, LC conditions, or mass spectrometer performance that require further investigation.
MS1 base peak chromatograms extracted from the spectrum files
The Base Peak Chromatogram (BPC) displays the intensity of the most abundant ion at each retention time point across your LC-MS run. Unlike the Total Ion Chromatogram (TIC) which shows the summed intensity of all ions, the BPC highlights the strongest signals, providing better visualization of compounds with high abundance while reducing baseline noise. This makes it particularly useful for identifying major components in complex samples, monitoring dominant species, and providing clearer peak visualization when signal-to-noise ratio is a concern. Comparing BPC patterns across samples allows you to evaluate consistency in the detection of high-abundance compounds and can reveal significant variations in sample composition or instrument performance.
MS1 Peaks from the spectrum files
This plot shows the number of peaks detected in MS1 scans over the course of each sample run. The x-axis represents retention time (in minutes), while the y-axis displays the number of distinct ion signals (peaks) identified in each MS1 scan. The MS1 peak count reflects spectral complexity and provides insight into instrument performance during the LC-MS analysis. Key aspects to consider include:
- Overall pattern: Peak counts typically increase during the elution of complex mixtures and decrease during column washing or re-equilibration phases.
- Peak density: Higher counts suggest more complex spectra, potentially indicating a greater number of compounds present at that time point."
- Peak Consistency across samples: Similar profiles among replicates or related samples indicate good analytical reproducibility.
- Sudden drops: Abrupt decreases in peak count may point to transient ionization issues, spray instability, or chromatographic disruptions.
- Baseline values: The minimum peak count observed reflects the level of background noise or instrument sensitivity in the absence of eluting compounds.
Monitoring MS1 peak counts complements total ion chromatogram (TIC) and base peak chromatogram (BPC) data, offering an additional layer of quality control related to signal complexity, instrument stability, and sample composition.
General stats for MS1 information extracted from the spectrum files
This table presents general statistics for MS1 information extracted from mass spectrometry data files." It displays MS runs with their acquisition dates and times. For each file, the table shows two key metrics: TotalCurrent (the sum of all MS1 ion intensities throughout the run) and ScanCurrent (the sum of MS2 ion intensities). These values provide a quick overview of the total ion signals detected during both survey scans (MS1) and fragmentation scans (MS2), allowing for comparison of overall signal intensity across samples. Consistent TotalCurrent and ScanCurrent values across similar samples typically indicate good reproducibility in the mass spectrometry analysis, while significant variations may suggest issues with sample preparation, instrument performance, or ionization efficiency. The blue shading helps visualize the relative intensity differences between samples.
| File | Acquisition Date Time | log10(Total Current) | log10(Scan Current) |
|---|---|---|---|
| a05058 | 2017-04-05 00:38:45 | 13.3186 | 10.7826 |
| a05059 | 2017-04-05 04:14:11 | 13.1799 | 10.6932 |
| a05060 | 2017-04-05 07:49:24 | 13.3878 | 10.7992 |
| a05061 | 2017-04-05 11:24:37 | 13.4434 | 10.8149 |
| a05062 | 2017-04-05 15:00:06 | 13.3927 | 10.8790 |
| a05063 | 2017-04-05 18:32:46 | 13.3876 | 10.9186 |
| a05064 | 2017-04-05 22:05:41 | 13.4376 | 10.9428 |
| a05065 | 2017-04-06 10:43:06 | 13.3235 | 10.8011 |
| a05066 | 2017-04-06 14:15:46 | 13.4091 | 10.8419 |
| a05067 | 2017-04-06 17:48:21 | 13.4054 | 10.8081 |
| a05068 | 2017-04-06 21:21:20 | 12.7353 | 10.4647 |
HeatMap
This heatmap shows a performance overview of the pipeline
This plot shows the pipeline performance overview. Some metrics are calculated.
- Heatmap score[Contaminants]: as fraction of summed intensity with 0 = sample full of contaminants; 1 = no contaminants
- Heatmap score[Pep Intensity (>23.0)]: Linear scale of the median intensity reaching the threshold, i.e. reaching 2^21 of 2^23 gives score 0.25.
- Heatmap score[Charge]: Deviation of the charge 2 proportion from a representative Raw file (median). For typtic digests, peptides of charge 2 (one N-terminal and one at tryptic C-terminal R or K residue) should be dominant. Ionization issues (voltage?), in-source fragmentation, missed cleavages and buffer irregularities can cause a shift (see Bittremieux 2017, DOI: 10.1002/mas.21544 ).
- Heatmap score [MC]: the fraction (0% - 100%) of fully cleaved peptides per Raw file
- Heatmap score [MC Var]: each Raw file is scored for its deviation from the ‘average’ digestion state of the current study.
- Heatmap score [ID rate over RT]: Judge column occupancy over retention time. Ideally, the LC gradient is chosen such that the number of identifications (here, after FDR filtering) is uniform over time, to ensure consistent instrument duty cycles. Sharp peaks and uneven distribution of identifications over time indicate potential for LC gradient optimization.Scored using ‘Uniform’ scoring function. i.e. constant receives good score, extreme shapes are bad.
- Heatmap score [MS2 Oversampling]: The percentage of non-oversampled 3D-peaks. An oversampled 3D-peak is defined as a peak whose peptide ion (same sequence and same charge state) was identified by at least two distinct MS2 spectra in the same Raw file. For high complexity samples, oversampling of individual 3D-peaks automatically leads to undersampling or even omission of other 3D-peaks, reducing the number of identified peptides.
- Heatmap score [Pep Missing]: Linear scale of the fraction of missing peptides.
Summary Table
This table shows the quantms pipeline summary statistics.
This table shows the quantms pipeline summary statistics.
| #MS2 Spectra | #Identified MS2 Spectra | %Identified MS2 Spectra | #Peptides Identified | #Proteins Identified | #Proteins Quantified |
|---|---|---|---|---|---|
| 433836 | 154772 | 35.68% | 90555 | 9655 | 9655 |
Pipeline Result Statistics
This plot shows the quantms pipeline final result.
Including Sample Name、Possible Study Variables、identified the number of peptide in the pipeline、
and identified the number of modified peptide in the pipeline, eg. All data in this table are obtained
from the out_msstats file. You can also remove the decoy with the remove_decoy parameter.
| Sample Name | MSstats Condition: SP | MSstats Condition: CT | MSstats Condition: QY | MSstats Condition: CV | Fraction | #Peptide IDs | #Unambiguous Peptide IDs | #Modified Peptide IDs | #Protein (group) IDs |
|---|---|---|---|---|---|---|---|---|---|
| 1 | Saccharomyces cerevisiae | Mixture | 10% | in-house | |||||
| 1 | 12495 | 11321 | 12495 | 5631 | |||||
| 2 | 13568 | 12325 | 13568 | 6045 | |||||
| 3 | 13003 | 11783 | 13003 | 5875 | |||||
| 4 | 13433 | 12260 | 13433 | 5902 | |||||
| 5 | 14216 | 12956 | 14216 | 6159 | |||||
| 6 | 18009 | 16369 | 18009 | 6420 | |||||
| 7 | 16285 | 14718 | 16285 | 6068 | |||||
| 8 | 14215 | 13004 | 14215 | 6077 | |||||
| 9 | 14554 | 13271 | 14554 | 6093 | |||||
| 10 | 13765 | 12537 | 13765 | 6024 | |||||
| 11 | 12 | 12 | 12 | 10 | |||||
| 2 | Saccharomyces cerevisiae | Mixture | 10% | in-house | |||||
| 1 | 12495 | 11321 | 12495 | 5631 | |||||
| 2 | 13568 | 12325 | 13568 | 6045 | |||||
| 3 | 13003 | 11783 | 13003 | 5875 | |||||
| 4 | 13433 | 12260 | 13433 | 5902 | |||||
| 5 | 14216 | 12956 | 14216 | 6159 | |||||
| 6 | 18009 | 16369 | 18009 | 6420 | |||||
| 7 | 16285 | 14718 | 16285 | 6068 | |||||
| 8 | 14215 | 13004 | 14215 | 6077 | |||||
| 9 | 14554 | 13271 | 14554 | 6093 | |||||
| 10 | 13765 | 12537 | 13765 | 6024 | |||||
| 11 | 12 | 12 | 12 | 10 | |||||
| 3 | Saccharomyces cerevisiae | Mixture | 10% | in-house | |||||
| 1 | 12495 | 11321 | 12495 | 5631 | |||||
| 2 | 13568 | 12325 | 13568 | 6045 | |||||
| 3 | 13003 | 11783 | 13003 | 5875 | |||||
| 4 | 13433 | 12260 | 13433 | 5902 | |||||
| 5 | 14216 | 12956 | 14216 | 6159 | |||||
| 6 | 18009 | 16369 | 18009 | 6420 | |||||
| 7 | 16285 | 14718 | 16285 | 6068 | |||||
| 8 | 14215 | 13004 | 14215 | 6077 | |||||
| 9 | 14554 | 13271 | 14554 | 6093 | |||||
| 10 | 13765 | 12537 | 13765 | 6024 | |||||
| 11 | 12 | 12 | 12 | 10 | |||||
| 4 | Saccharomyces cerevisiae | Mixture | 5% | in-house | |||||
| 1 | 12495 | 11321 | 12495 | 5631 | |||||
| 2 | 13568 | 12325 | 13568 | 6045 | |||||
| 3 | 13003 | 11783 | 13003 | 5875 | |||||
| 4 | 13433 | 12260 | 13433 | 5902 | |||||
| 5 | 14216 | 12956 | 14216 | 6159 | |||||
| 6 | 18009 | 16369 | 18009 | 6420 | |||||
| 7 | 16285 | 14718 | 16285 | 6068 | |||||
| 8 | 14215 | 13004 | 14215 | 6077 | |||||
| 9 | 14554 | 13271 | 14554 | 6093 | |||||
| 10 | 13765 | 12537 | 13765 | 6024 | |||||
| 11 | 12 | 12 | 12 | 10 | |||||
| 5 | Saccharomyces cerevisiae | Mixture | 5% | in-house | |||||
| 1 | 12495 | 11321 | 12495 | 5631 | |||||
| 2 | 13568 | 12325 | 13568 | 6045 | |||||
| 3 | 13003 | 11783 | 13003 | 5875 | |||||
| 4 | 13433 | 12260 | 13433 | 5902 | |||||
| 5 | 14216 | 12956 | 14216 | 6159 | |||||
| 6 | 18009 | 16369 | 18009 | 6420 | |||||
| 7 | 16285 | 14718 | 16285 | 6068 | |||||
| 8 | 14215 | 13004 | 14215 | 6077 | |||||
| 9 | 14554 | 13271 | 14554 | 6093 | |||||
| 10 | 13765 | 12537 | 13765 | 6024 | |||||
| 11 | 12 | 12 | 12 | 10 | |||||
| 6 | Saccharomyces cerevisiae | Mixture | 5% | in-house | |||||
| 1 | 12495 | 11321 | 12495 | 5631 | |||||
| 2 | 13568 | 12325 | 13568 | 6045 | |||||
| 3 | 13003 | 11783 | 13003 | 5875 | |||||
| 4 | 13433 | 12260 | 13433 | 5902 | |||||
| 5 | 14216 | 12956 | 14216 | 6159 | |||||
| 6 | 18009 | 16369 | 18009 | 6420 | |||||
| 7 | 16285 | 14718 | 16285 | 6068 | |||||
| 8 | 14215 | 13004 | 14215 | 6077 | |||||
| 9 | 14554 | 13271 | 14554 | 6093 | |||||
| 10 | 13765 | 12537 | 13765 | 6024 | |||||
| 11 | 12 | 12 | 12 | 10 | |||||
| 7 | Saccharomyces cerevisiae | Mixture | 5% | in-house | |||||
| 1 | 12495 | 11321 | 12495 | 5631 | |||||
| 2 | 13568 | 12325 | 13568 | 6045 | |||||
| 3 | 13003 | 11783 | 13003 | 5875 | |||||
| 4 | 13433 | 12260 | 13433 | 5902 | |||||
| 5 | 14216 | 12956 | 14216 | 6159 | |||||
| 6 | 18009 | 16369 | 18009 | 6420 | |||||
| 7 | 16285 | 14718 | 16285 | 6068 | |||||
| 8 | 14215 | 13004 | 14215 | 6077 | |||||
| 9 | 14554 | 13271 | 14554 | 6093 | |||||
| 10 | 13765 | 12537 | 13765 | 6024 | |||||
| 11 | 12 | 12 | 12 | 10 | |||||
| 8 | Saccharomyces cerevisiae | Mixture | 3.3% | in-house | |||||
| 1 | 12495 | 11321 | 12495 | 5631 | |||||
| 2 | 13568 | 12325 | 13568 | 6045 | |||||
| 3 | 13003 | 11783 | 13003 | 5875 | |||||
| 4 | 13433 | 12260 | 13433 | 5902 | |||||
| 5 | 14216 | 12956 | 14216 | 6159 | |||||
| 6 | 18009 | 16369 | 18009 | 6420 | |||||
| 7 | 16285 | 14718 | 16285 | 6068 | |||||
| 8 | 14215 | 13004 | 14215 | 6077 | |||||
| 9 | 14554 | 13271 | 14554 | 6093 | |||||
| 10 | 13765 | 12537 | 13765 | 6024 | |||||
| 11 | 12 | 12 | 12 | 10 | |||||
| 9 | Saccharomyces cerevisiae | Mixture | 3.3% | in-house | |||||
| 1 | 12495 | 11321 | 12495 | 5631 | |||||
| 2 | 13568 | 12325 | 13568 | 6045 | |||||
| 3 | 13003 | 11783 | 13003 | 5875 | |||||
| 4 | 13433 | 12260 | 13433 | 5902 | |||||
| 5 | 14216 | 12956 | 14216 | 6159 | |||||
| 6 | 18009 | 16369 | 18009 | 6420 | |||||
| 7 | 16285 | 14718 | 16285 | 6068 | |||||
| 8 | 14215 | 13004 | 14215 | 6077 | |||||
| 9 | 14554 | 13271 | 14554 | 6093 | |||||
| 10 | 13765 | 12537 | 13765 | 6024 | |||||
| 11 | 12 | 12 | 12 | 10 | |||||
| 10 | Saccharomyces cerevisiae | Mixture | 3.3% | in-house | |||||
| 1 | 12495 | 11321 | 12495 | 5631 | |||||
| 2 | 13568 | 12325 | 13568 | 6045 | |||||
| 3 | 13003 | 11783 | 13003 | 5875 | |||||
| 4 | 13433 | 12260 | 13433 | 5902 | |||||
| 5 | 14216 | 12956 | 14216 | 6159 | |||||
| 6 | 18009 | 16369 | 18009 | 6420 | |||||
| 7 | 16285 | 14718 | 16285 | 6068 | |||||
| 8 | 14215 | 13004 | 14215 | 6077 | |||||
| 9 | 14554 | 13271 | 14554 | 6093 | |||||
| 10 | 13765 | 12537 | 13765 | 6024 | |||||
| 11 | 12 | 12 | 12 | 10 | |||||
| 11 | Saccharomyces cerevisiae | Mixture | 3.3% | in-house | |||||
| 1 | 12495 | 11321 | 12495 | 5631 | |||||
| 2 | 13568 | 12325 | 13568 | 6045 | |||||
| 3 | 13003 | 11783 | 13003 | 5875 | |||||
| 4 | 13433 | 12260 | 13433 | 5902 | |||||
| 5 | 14216 | 12956 | 14216 | 6159 | |||||
| 6 | 18009 | 16369 | 18009 | 6420 | |||||
| 7 | 16285 | 14718 | 16285 | 6068 | |||||
| 8 | 14215 | 13004 | 14215 | 6077 | |||||
| 9 | 14554 | 13271 | 14554 | 6093 | |||||
| 10 | 13765 | 12537 | 13765 | 6024 | |||||
| 11 | 12 | 12 | 12 | 10 |
Number of Peptides identified Per Protein
This plot shows the number of peptides per protein in quantms pipeline final result
This statistic is extracted from the out_msstats file. Proteins supported by more peptide identifications can constitute more confident results.
Spectra Tracking
This plot shows the tracking of the number of spectra along the quantms pipeline
This table shows the changes in the number of spectra corresponding to each input file
during the pipeline operation. And the number of peptides finally identified and quantified is obtained from
the PSM table in the mzTab file. You can also remove decoys with the remove_decoy parameter.:
- MS1_Num: The number of MS1 spectra extracted from mzMLs
- MS2_Num: The number of MS2 spectra extracted from mzMLs
- MSGF: The Number of spectra identified by MSGF search engine
- Comet: The Number of spectra identified by Comet search engine
- Sage: The Number of spectra identified by Sage search engine
- PSMs from quant. peptides: extracted from PSM table in mzTab file
- Peptides quantified: extracted from PSM table in mzTab file
| Spectra File | #MS1 Spectra | #MS2 Spectra | MSGF | Comet | #PSMs from quant. peptides | #Peptides quantified |
|---|---|---|---|---|---|---|
| a05058 | 6870 | 37330 | 24401 | 24117 | 13935 | 11763 |
| a05059 | 6471 | 37536 | 24920 | 24702 | 14683 | 13183 |
| a05060 | 7266 | 38047 | 24711 | 24518 | 14027 | 12475 |
| a05061 | 7649 | 37733 | 24986 | 24790 | 14661 | 12995 |
| a05062 | 5657 | 41445 | 26957 | 26729 | 15121 | 13672 |
| a05063 | 5982 | 42856 | 29469 | 29222 | 18909 | 17336 |
| a05064 | 7075 | 40809 | 27720 | 27427 | 17667 | 15735 |
| a05065 | 5947 | 40698 | 26495 | 26127 | 15303 | 13323 |
| a05066 | 6051 | 41078 | 26992 | 26761 | 15630 | 13808 |
| a05067 | 6062 | 39997 | 26228 | 25738 | 14819 | 13170 |
| a05068 | 4297 | 36307 | 17727 | 17634 | 17 | 12 |
Summary of Search Engine Scores
These plots contain search scores and PEPs counts for different search engines in different files, and they also contain a summary of the consensus PSMs if two or more search engines are used.
SpecEvalue Description
This statistic is extracted from idXML files. SpecEvalue: Spectral E-values, the search score of MSGF. The value used for plotting is -lg(SpecEvalue).
xcorr description
This statistic is extracted from idXML files. xcorr: cross-correlation scores, the search score of Comet. The value used for plotting is xcorr.
Summary of Posterior Error Probabilities (PEP)
This statistic is extracted from idXML files.
Summary of consensus support for PSMs
Consensus support is a measure of agreement between search engines. Every peptide sequence in the analysis has been identified by at least one search run. The consensus support defines which fraction (between 0 and 1) of the remaining search runs "supported" a peptide identification that was kept. The meaning of "support" differs slightly between algorithms: For best, worst, average and rank, each search run supports peptides that it has also identified among its top considered_hits candidates. So the "consensus support" simply gives the fraction of additional search engines that have identified a peptide. (For example, if there are three search runs, peptides identified by two of them will have a "support" of 0.5.) For the similarity-based algorithms PEPMatrix and PEPIons, the "support" for a peptide is the average similarity of the most-similar peptide from each (other) search run.
Distribution of precursor charges
This is a bar chart representing the distribution of the precursor ion charges for a given whole experiment.
This information can be used to identify potential ionization problems including many 1+ charges from an ESI ionization source or an unexpected distribution of charges. MALDI experiments are expected to contain almost exclusively 1+ charged ions. An unexpected charge distribution may furthermore be caused by specific search engine parameter settings such as limiting the search to specific ion charges.
Number of Peaks per MS/MS spectrum
This chart represents a histogram containing the number of peaks per MS/MS spectrum in a given experiment.
This chart assumes centroid data. Too few peaks can identify poor fragmentation or a detector fault, as opposed to a large number of peaks representing very noisy spectra. This chart is extensively dependent on the pre-processing steps performed to the spectra (centroiding, deconvolution, peak picking approach, etc).
Peak Intensity Distribution
This is a histogram representing the ion intensity vs. the frequency for all MS2 spectra in a whole given experiment. It is possible to filter the information for all, identified and unidentified spectra. This plot can give a general estimation of the noise level of the spectra.
Generally, one should expect to have a high number of low intensity noise peaks with a low number of high intensity signal peaks. A disproportionate number of high signal peaks may indicate heavy spectrum pre-filtering or potential experimental problems. In the case of data reuse this plot can be useful in identifying the requirement for pre-processing of the spectra prior to any downstream analysis. The quality of the identifications is not linked to this data as most search engines perform internal spectrum pre-processing before matching the spectra. Thus, the spectra reported are not necessarily pre-processed since the search engine may have applied the pre-processing step internally. This pre-processing is not necessarily reported in the experimental metadata.
Oversampling Distribution
An oversampled 3D-peak is defined as a peak whose peptide ion (same sequence and same charge state) was identified by at least two distinct MS2 spectra in the same Raw file.
For high complexity samples, oversampling of individual 3D-peaks automatically leads to undersampling or even omission of other 3D-peaks, reducing the number of identified peptides. Oversampling occurs in low-complexity samples or long LC gradients, as well as undersized dynamic exclusion windows for data independent acquisitions.
- Heatmap score [EVD: MS2 Oversampling]: The percentage of non-oversampled 3D-peaks.
Delta Mass
This chart represents the distribution of the relative frequency of experimental precursor ion mass (m/z) - theoretical precursor ion mass (m/z).
Mass deltas close to zero reflect more accurate identifications and also that the reporting of the amino acid modifications and charges have been done accurately. This plot can highlight systematic bias if not centered on zero. Other distributions can reflect modifications not being reported properly. Also it is easy to see the different between the target and the decoys identifications.
Peptides Quantification Table
This plot shows the quantification information of peptides in the final result (mainly the mzTab file).
The quantification information of peptides is obtained from the MSstats input file. The table shows the quantitative level and distribution of peptides in different study variables, run and peptiforms. The distribution show all the intensity values in a bar plot above and below the average intensity for all the fractions, runs and peptiforms.
- BestSearchScore: It is equal to 1 - min(Q.Value) for DIA datasets. Then it is equal to 1 - min(best_search_engine_score[1]), which is from best_search_engine_score[1] column in mzTab peptide table for DDA datasets.
- Average Intensity: Average intensity of each peptide sequence across all conditions with NA=0 or NA ignored.
- Peptide intensity in each condition (Eg.
CT=Mixture;CN=UPS1;QY=0.1fmol): Summarize intensity of fractions, and then mean intensity in technical replicates/biological replicates separately.
| PeptideID | Protein Name | Peptide Sequence | Best Search Score | Average Intensity | SP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-house | SP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-house | SP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-house |
|---|---|---|---|---|---|---|---|
| 1 | sp|P55011|S12A2_HUMAN | AAAAAAAAAAAAAAAGAGAGAK | 0.9999 | 5.1101 | 5.0860 | 5.1404 | 5.0960 |
| 2 | sp|Q99453|PHX2B_HUMAN | AAAAAAAAAK | 1.0000 | 5.9295 | 5.9276 | 5.9481 | 5.9117 |
| 3 | sp|Q96JP5|ZFP91_HUMAN | AAAAAAAAAVSR | 1.0000 | 4.2500 | 4.2237 | 4.2531 | 4.2656 |
| 4 | sp|Q5TF21|SOGA3_HUMAN | AAAAAAAAQMHAK | 1.0000 | 4.9208 | 4.8813 | 4.9496 | 4.9193 |
| 5 | sp|Q9Y4H2|IRS2_HUMAN | AAAAAAAAVPSAGPAGPAPTSAAGR | 1.0000 | 4.6795 | 4.6525 | 4.7113 | 4.6659 |
| 6 | sp|P36578|RL4_HUMAN | AAAAAAALQAK | 1.0000 | 5.6602 | 5.6780 | 5.6812 | 5.6235 |
| 7 | sp|O00178|GTPB1_HUMAN | AAAAAAR | 0.9997 | 4.1917 | 4.0798 | 4.2682 | 4.1818 |
| 8 | sp|Q6SPF0|SAMD1_HUMAN | AAAAAATAPPSPGPAQPGPR | 0.9970 | 4.5783 | 4.5565 | 4.5829 | 4.5895 |
| 9 | sp|O76031|CLPX_HUMAN | AAAAADLANR | 1.0000 | 4.9044 | 4.8651 | 4.9259 | 4.9106 |
| 10 | sp|Q8WUQ7|CATIN_HUMAN | AAAAALSQQQSLQER | 1.0000 | 3.5486 | 3.4986 | 3.5609 | 3.5710 |
| 11 | sp|A6NIH7|U119B_HUMAN | AAAAASAAGPGGLVAGK | 1.0000 | 4.5009 | 4.4867 | 4.5216 | 4.4900 |
| 12 | sp|Q9BTD8|RBM42_HUMAN | AAAAATVVPPMVGGPPFVGPVGFGPGDR | 0.9997 | 4.1653 | 4.1245 | 4.1983 | 4.1603 |
| 13 | sp|Q9P258|RCC2_HUMAN | AAAAAWEEPSSGNGTAR | 1.0000 | 4.8387 | 4.8197 | 4.8616 | 4.8291 |
| 14 | sp|Q99615|DNJC7_HUMAN | AAAAECDVVMAATEPELLDDQEAK | 0.9989 | 4.3740 | 4.3483 | 4.3851 | 4.3813 |
| 15 | sp|Q9Y2U8|MAN1_HUMAN | AAAAGSLDR | 0.9999 | 4.9444 | 4.9107 | 4.9686 | 4.9437 |
| 16 | sp|P0C0T4|RS25B_YEAST;sp|Q3E792|RS25A_YEAST | AAAALAGGK | 0.9999 | 5.8076 | 6.0928 | 5.7184 | 5.4974 |
| 17 | sp|Q15596|NCOA2_HUMAN | AAAANIDEVQK | 1.0000 | 4.1618 | 4.1756 | 4.1710 | 4.1415 |
| 18 | sp|Q9UPT8|ZC3H4_HUMAN | AAAAPAATTATPPPEGAPPQPGVHNLPVPTLFGTVK | 1.0000 | 4.4684 | 4.4335 | 4.5097 | 4.4498 |
| 19 | sp|Q96L91|EP400_HUMAN | AAAAPFQTSQASASAPR | 0.9997 | 4.2268 | 4.1954 | 4.2729 | 4.2001 |
| 20 | sp|P52701|MSH6_HUMAN | AAAAPGASPSPGGDAAWSEAGPGPR | 1.0000 | 5.3677 | 5.4158 | 5.3708 | 5.3244 |
| 21 | sp|P52701|MSH6_HUMAN | AAAAPGASPSPGGDAAWSEAGPGPRPLAR | 1.0000 | 3.5832 | 3.5465 | 3.6371 | 3.5511 |
| 22 | sp|P55036|PSMD4_HUMAN | AAAASAAEAGIATTGTEDSDDALLK | 1.0000 | 4.9622 | 4.9446 | 4.9947 | 4.9408 |
| 23 | sp|P09938|RIR2_YEAST | AAADALSDLEIK | 0.9997 | 4.8986 | 5.1140 | 4.8541 | 4.6881 |
| 24 | sp|O95159|ZFPL1_HUMAN | AAADSDPNLDPLMNPHIR | 1.0000 | 5.1045 | 5.0664 | 5.1372 | 5.0980 |
| 25 | sp|Q6P2E9|EDC4_HUMAN | AAADTLQGPMQAAYR | 1.0000 | 3.6096 | 3.5992 | 3.6228 | 3.6039 |
| 26 | sp|Q6P2E9|EDC4_HUMAN | AAADTLQGPMQAAYR | 1.0000 | 3.3063 | 3.2023 | 3.3229 | 3.3557 |
| 27 | sp|Q9NQP4|PFD4_HUMAN | AAAEDVNVTFEDQQK | 1.0000 | 4.0292 | 3.9906 | 4.0576 | 4.0276 |
| 28 | sp|O95551|TYDP2_HUMAN | AAAEEGHIIPR | 1.0000 | 5.4478 | 5.3897 | 5.4833 | 5.4515 |
| 29 | sp|O15357|SHIP2_HUMAN | AAAEELLAR | 1.0000 | 5.0724 | 5.0563 | 5.0820 | 5.0745 |
| 30 | sp|Q9H9Y2|RPF1_HUMAN | AAAEELQEAAGAGDGATENGVQPPK | 1.0000 | 4.5297 | 4.4950 | 4.5624 | 4.5206 |
| 31 | sp|Q96P70|IPO9_HUMAN | AAAEEQIK | 0.9999 | 5.2276 | 5.1954 | 5.2506 | 5.2273 |
| 32 | sp|P30260|CDC27_HUMAN | AAAEGLMSLLR | 1.0000 | 4.3024 | 4.2771 | 4.3361 | 4.2854 |
| 33 | sp|P00360|G3P1_YEAST | AAAEGPMK | 0.9988 | 3.9138 | 4.1444 | 3.8283 | 3.7290 |
| 34 | sp|P00360|G3P1_YEAST | AAAEGPMK | 1.0000 | 4.7633 | 5.0495 | 4.6743 | 4.4495 |
| 35 | sp|P15180|SYKC_YEAST | AAAEGVANLHLDEATGEMVSK | 1.0000 | 4.2037 | 4.4023 | 4.1753 | 4.0020 |
| 36 | sp|P15180|SYKC_YEAST | AAAEGVANLHLDEATGEMVSK | 1.0000 | 5.0252 | 5.2850 | 4.9685 | 4.7316 |
| 37 | sp|Q9NP50|SHCAF_HUMAN | AAAEKPEEQGPEPLPISTQEW | 1.0000 | 4.6442 | 4.6190 | 4.6637 | 4.6425 |
| 38 | sp|Q01780|EXOSX_HUMAN | AAAEQAISVR | 1.0000 | 4.9211 | 4.9080 | 4.9425 | 4.9085 |
| 39 | sp|O94766|B3GA3_HUMAN | AAAEQLR | 0.9998 | 4.8666 | 4.8356 | 4.8987 | 4.8555 |
| 40 | sp|Q02880|TOP2B_HUMAN | AAAERPK | 0.9991 | 5.2989 | 5.2501 | 5.3288 | 5.3027 |
| 41 | sp|P02786|TFR1_HUMAN | AAAEVAGQFVIK | 0.9999 | 5.7815 | 5.7528 | 5.8144 | 5.7681 |
| 42 | sp|P07954|FUMH_HUMAN | AAAEVNQDYGLDPK | 1.0000 | 5.1767 | 5.1675 | 5.1999 | 5.1594 |
| 43 | sp|P15705|STI1_YEAST | AAAEYEK | 1.0000 | 4.8083 | 5.0531 | 4.7440 | 4.5642 |
| 44 | sp|Q9Y490|TLN1_HUMAN | AAAFEEQENETVVVK | 1.0000 | 5.1944 | 5.1751 | 5.2089 | 5.1939 |
| 45 | sp|Q9P2E9|RRBP1_HUMAN | AAAFEK | 0.9998 | 5.5448 | 5.5160 | 5.5730 | 5.5365 |
| 46 | sp|O94826|TOM70_HUMAN | AAAFEQLQK | 1.0000 | 5.0643 | 5.0542 | 5.0947 | 5.0397 |
| 47 | sp|Q9H9Y2|RPF1_HUMAN | AAAFPPGFSISEIK | 1.0000 | 4.4674 | 4.4606 | 4.4868 | 4.4522 |
| 48 | sp|Q9Y6X3|SCC4_HUMAN | AAAFYVR | 0.9997 | 4.4727 | 4.4467 | 4.4918 | 4.4721 |
| 49 | sp|Q9P2E9|RRBP1_HUMAN | AAAGEAK | 1.0000 | 4.3334 | 4.2981 | 4.3611 | 4.3302 |
| 50 | sp|P23381|SYWC_HUMAN | AAAGEDYK | 1.0000 | 5.1423 | 5.1080 | 5.1395 | 5.1689 |
Protein Quantification Table
This plot shows the quantification information of proteins in the final result (mainly the mzTab file).
The quantification information of proteins is obtained from the msstats input file. The table shows the quantitative level and distribution of proteins in different study variables and run.
- Peptides_Number: The number of peptides for each protein.
- Average Intensity: Average intensity of each protein across all conditions with NA=0 or NA ignored.
- Protein intensity in each condition (Eg.
CT=Mixture;CN=UPS1;QY=0.1fmol): Summarize intensity of peptides.
| ProteinID | Protein Name | Number of Peptides | Average Intensity | SP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-house | SP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-house | SP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-house |
|---|---|---|---|---|---|---|
| 1 | sp|A0A096LP55|QCR6L_HUMAN;sp|P07919|QCR6_HUMAN | 1 | 3.7629 | 3.7228 | 3.7953 | 3.7581 |
| 2 | sp|A0A0B4J2D5|GAL3B_HUMAN;sp|P0DPI2|GAL3A_HUMAN | 9 | 6.5573 | 6.5406 | 6.5786 | 6.5475 |
| 3 | sp|A0A0B4J2F0|PIOS1_HUMAN | 1 | 4.2780 | 4.2463 | 4.3042 | 4.2739 |
| 4 | sp|A0AVF1|IFT56_HUMAN | 3 | 4.4387 | 4.4337 | 4.4436 | 4.4376 |
| 5 | sp|A0AVT1|UBA6_HUMAN | 31 | 6.7475 | 6.7247 | 6.7693 | 6.7418 |
| 6 | sp|A0FGR8|ESYT2_HUMAN | 15 | 6.2588 | 6.2497 | 6.2776 | 6.2462 |
| 7 | sp|A0JNW5|UH1BL_HUMAN | 5 | 5.2052 | 5.1740 | 5.2309 | 5.2013 |
| 8 | sp|A0MZ66|SHOT1_HUMAN | 27 | 6.3095 | 6.2787 | 6.3350 | 6.3057 |
| 9 | sp|A0PJW6|TM223_HUMAN | 3 | 5.4129 | 5.3812 | 5.4432 | 5.4043 |
| 10 | sp|A0PK00|T120B_HUMAN | 1 | 4.7299 | 4.7075 | 4.7537 | 4.7216 |
| 11 | sp|A1A4S6|RHG10_HUMAN | 6 | 5.5921 | 5.5618 | 5.6207 | 5.5843 |
| 12 | sp|A1IGU5|ARH37_HUMAN | 1 | 4.5503 | 4.5026 | 4.5592 | 4.5746 |
| 13 | sp|A1L020|MEX3A_HUMAN | 9 | 6.0197 | 5.9861 | 6.0425 | 6.0206 |
| 14 | sp|A1L0T0|HACL2_HUMAN | 14 | 6.1952 | 6.1741 | 6.2165 | 6.1891 |
| 15 | sp|A1L157|TSN11_HUMAN | 1 | 4.4176 | 4.3933 | 4.4480 | 4.4036 |
| 16 | sp|A1L170|CA226_HUMAN | 1 | 4.3816 | 4.3458 | 4.3944 | 4.3942 |
| 17 | sp|A1L390|PKHG3_HUMAN | 5 | 5.0416 | 4.9997 | 5.0701 | 5.0423 |
| 18 | sp|A1X283|SPD2B_HUMAN | 36 | 6.7276 | 6.7006 | 6.7492 | 6.7250 |
| 19 | sp|A1XBS5|FA92A_HUMAN | 1 | 3.8100 | 3.7434 | 3.8548 | 3.8091 |
| 20 | sp|A2AJT9|BCLA3_HUMAN | 3 | 5.1031 | 5.0738 | 5.1206 | 5.1064 |
| 21 | sp|A2RRD8|ZN320_HUMAN | 1 | 4.3234 | 4.2796 | 4.3412 | 4.3363 |
| 22 | sp|A2RRP1|NBAS_HUMAN | 30 | 6.4328 | 6.3973 | 6.4582 | 6.4323 |
| 23 | sp|A2RTX5|SYTC2_HUMAN | 1 | 4.1704 | 4.1527 | 4.1942 | 4.1588 |
| 24 | sp|A2RU67|F234B_HUMAN | 2 | 4.7223 | 4.7009 | 4.7357 | 4.7243 |
| 25 | sp|A2RUC4|TYW5_HUMAN | 4 | 5.0917 | 5.0634 | 5.1187 | 5.0844 |
| 26 | sp|A3KMH1|VWA8_HUMAN | 33 | 6.4954 | 6.5007 | 6.5080 | 6.4784 |
| 27 | sp|A3KN83|SBNO1_HUMAN | 18 | 6.1917 | 6.1675 | 6.2129 | 6.1877 |
| 28 | sp|A4D161|F221A_HUMAN | 5 | 5.2597 | 5.2262 | 5.2892 | 5.2533 |
| 29 | sp|A4D1E9|GTPBA_HUMAN | 5 | 5.6777 | 5.6564 | 5.6990 | 5.6714 |
| 30 | sp|A4D1P6|WDR91_HUMAN | 13 | 5.9108 | 5.8814 | 5.9328 | 5.9095 |
| 31 | sp|A4D1U4|DEN11_HUMAN | 3 | 4.5285 | 4.4789 | 4.5649 | 4.5257 |
| 32 | sp|A4D2B0|MBLC1_HUMAN | 2 | 4.1057 | 4.0507 | 4.1030 | 4.1454 |
| 33 | sp|A5D8V6|VP37C_HUMAN | 3 | 5.1016 | 5.0754 | 5.1207 | 5.1012 |
| 34 | sp|A5PLL7|PDES1_HUMAN | 2 | 5.1872 | 5.1639 | 5.2028 | 5.1883 |
| 35 | sp|A5PLN9|TPC13_HUMAN | 3 | 5.6313 | 5.5989 | 5.6598 | 5.6251 |
| 36 | sp|A5YKK6|CNOT1_HUMAN | 53 | 6.9213 | 6.8919 | 6.9446 | 6.9186 |
| 37 | sp|A6H8Y1|BDP1_HUMAN | 2 | 4.9599 | 4.9276 | 4.9915 | 4.9504 |
| 38 | sp|A6NC57|ANR62_HUMAN | 1 | 3.3462 | 3.2325 | 3.3558 | 3.4070 |
| 39 | sp|A6NCE7|MP3B2_HUMAN;sp|Q9GZQ8|MLP3B_HUMAN | 2 | 5.3332 | 5.3261 | 5.3676 | 5.3015 |
| 40 | sp|A6NCS6|CB072_HUMAN | 4 | 4.7068 | 4.6902 | 4.7139 | 4.7118 |
| 41 | sp|A6ND36|FA83G_HUMAN | 3 | 4.9101 | 4.9036 | 4.9309 | 4.8935 |
| 42 | sp|A6NDB9|PALM3_HUMAN | 11 | 5.7112 | 5.6822 | 5.7320 | 5.7110 |
| 43 | sp|A6NDE4|RBY1B_HUMAN;sp|A6NEQ0|RBY1E_HUMAN;sp|P0C7P1|RBY1D_HUMAN;sp|P0DJD3|RBY1A_HUMAN;sp|P0DJD4|RBY1C_HUMAN;sp|Q15415|RBY1F_HUMAN | 1 | 4.7747 | 4.7245 | 4.7941 | 4.7901 |
| 44 | sp|A6NDG6|PGP_HUMAN | 5 | 5.8649 | 5.8390 | 5.8840 | 5.8643 |
| 45 | sp|A6NDU8|CE051_HUMAN | 2 | 4.8114 | 4.7871 | 4.8268 | 4.8133 |
| 46 | sp|A6NDX5|ZN840_HUMAN | 1 | 4.3298 | 4.2876 | 4.3691 | 4.3187 |
| 47 | sp|A6NED2|RCCD1_HUMAN | 3 | 4.7508 | 4.7096 | 4.7662 | 4.7645 |
| 48 | sp|A6NFI3|ZN316_HUMAN | 2 | 4.9098 | 4.8857 | 4.9296 | 4.9071 |
| 49 | sp|A6NGN9|IGLO5_HUMAN | 2 | 5.0687 | 5.0540 | 5.0837 | 5.0642 |
| 50 | sp|A6NHL2|TBAL3_HUMAN | 1 | 4.0439 | 3.9831 | 4.0709 | 4.0582 |
bigbio/quantms Methods Description
Suggested text and references to use when describing pipeline usage within the methods section of a publication.URL: https://github.com/bigbio/quantms
Methods
Data was processed using bigbio/quantms v1.4.0dev (doi: 10.5281/zenodo.7754148) of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.
The pipeline was executed with Nextflow v24.10.5 (Di Tommaso et al., 2017) with the following command:
nextflow run main.nf --input /mnt/daicx/pvc-afbfaa68-aa52-416c-b273-64fb016fd745/mcp/PXD007683/PXD007683-LFQ.sdrf.tsv --database /mnt/daicx/pvc-afbfaa68-aa52-416c-b273-64fb016fd745/mcp/PXD007683/uniprot-UP000005640_UP000002311_reviewed.fasta --add_decoys true --search_engines msgf,comet -resume PXD007683 -c /mnt/daicx/pvc-afbfaa68-aa52-416c-b273-64fb016fd745/mcp/k8s_next.config -profile docker --ms2rescore true --ms2pip_model_dir /mnt/daicx/pvc-afbfaa68-aa52-416c-b273-64fb016fd745/model_file/ --root_folder /mnt/daicx/pvc-afbfaa68-aa52-416c-b273-64fb016fd745/mcp/PXD007683 --local_input_type raw --ms2pip_model HCD --outdir ./PXD007683_msgf_comet_ms2rescore_quant --skip_post_msstats true
References
- Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: 10.1038/nbt.3820
- Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: 10.1038/s41587-020-0439-x
- Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7
- da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: 10.1093/bioinformatics/btx192
Notes:
- The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
- You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.
Software Versions
Software Versions lists versions of software tools extracted from file contents.
| Group | Software | Version |
|---|---|---|
| CONSENSUSID | ConsensusID | 3.3.0-pre-exported-20250122 |
| DECOYDATABASE | DecoyDatabase | 3.3.0-pre-exported-20250122 |
| FDRCONSENSUSID | FalseDiscoveryRate | 3.3.0-pre-exported-20250122 |
| IDFILTER | IDFilter | 3.3.0-pre-exported-20250122 |
| MS2RESCORE | MS2Rescore | 3.1.4 |
| deeplc | 3.1.8 | |
| ms2pip | 4.1.0 | |
| quantms-rescoring | 0.0.5 | |
| MSGFDBINDEXING | msgf_plus | MS-GF+ Release (v2024.03.26) (26 March 2024) |
| MZMLSTATISTICS | quantms-utils | 0.0.20 |
| PERCOLATOR | PercolatorAdapter | 3.3.0-pre-exported-20250122 |
| percolator | 3.05.0, Build Date Aug 31 2020 19:03:04 | |
| PROTEOMICSLFQ | ProteomicsLFQ | 3.3.0-pre-exported-20250122 |
| SAMPLESHEET_CHECK | quantms-utils | 0.0.20 |
| SDRFPARSING | sdrf-pipelines | 0.0.31 |
| SEARCHENGINECOMET | Comet | 2023.01 rev. 2 |
| CometAdapter | 3.3.0-pre-exported-20250122 | |
| SEARCHENGINEMSGF | MSGFPlusAdapter | 3.3.0-pre-exported-20250122 |
| msgf_plus | MS-GF+ Release (v2023.01.12) (12 January 2023) | |
| THERMORAWFILEPARSER | ThermoRawFileParser | 1.3.4 |
| Workflow | Nextflow | 24.10.5 |
| bigbio/quantms | v1.4.0dev |
bigbio/quantms Workflow Summary
- this information is collected when the pipeline is started.URL: https://github.com/bigbio/quantms
Input/output options
- export_decoy_psm
- true
- input
- /mnt/daicx/pvc-afbfaa68-aa52-416c-b273-64fb016fd745/mcp/PXD007683/PXD007683-LFQ.sdrf.tsv
- local_input_type
- raw
- outdir
- ./PXD007683_msgf_comet_ms2rescore_quant
- root_folder
- /mnt/daicx/pvc-afbfaa68-aa52-416c-b273-64fb016fd745/mcp/PXD007683
SDRF validation
- skip_factor_validation
- true
- use_ols_cache_only
- true
- validate_ontologies
- true
Protein database
- add_decoys
- true
- database
- /mnt/daicx/pvc-afbfaa68-aa52-416c-b273-64fb016fd745/mcp/PXD007683/uniprot-UP000005640_UP000002311_reviewed.fasta
Database search
- search_engines
- msgf,comet
Modification localization
- luciphor_debug
- 0
PSM re-scoring (general)
- ms2pip_model
- HCD
- ms2pip_model_dir
- /mnt/daicx/pvc-afbfaa68-aa52-416c-b273-64fb016fd745/model_file/
- ms2rescore
- true
- run_fdr_cutoff
- 0.10
PSM re-scoring (Percolator)
- description_correct_features
- 0
Consensus ID
- consensusid_considered_top_hits
- 0
- min_consensus_support
- 0
Isobaric analyzer
- quant_activation_method
- HCD
Protein Quantification (LFQ)
- feature_with_id_min_score
- 0.10
Statistical post-processing
- contrasts
- pairwise
- skip_post_msstats
- true
Quality control
- enable_pmultiqc
- true
- pmultiqc_idxml_skip
- true
Generic options
- trace_report_suffix
- 2025-03-30_11-14-03
Core Nextflow options
- configFiles
- /mnt/daicx/pvc-afbfaa68-aa52-416c-b273-64fb016fd745/mcp/gitrepo/new_quantms/quantms/nextflow.config, /mnt/daicx/pvc-afbfaa68-aa52-416c-b273-64fb016fd745/mcp/k8s_next.config
- containerEngine
- docker
- launchDir
- /mnt/daicx/pvc-afbfaa68-aa52-416c-b273-64fb016fd745/mcp/gitrepo/new_quantms/quantms
- profile
- docker
- projectDir
- /mnt/daicx/pvc-afbfaa68-aa52-416c-b273-64fb016fd745/mcp/gitrepo/new_quantms/quantms
- runName
- mad_hodgkin
- userName
- daicx
- workDir
- /mnt/daicx/pvc-afbfaa68-aa52-416c-b273-64fb016fd745/mcp/gitrepo/new_quantms/quantms/work